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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[1.0.0b2] - 2025-12-02

Added

  • Comprehensive test suites for utilities, Manager, and Tools modules
    • Added 20+ test methods for BlastUtils, GenbankUtils, OrthologUtils, ManagerUtils, PackageVersion, and FullUtilities classes
    • Added 16 test methods for Management, RepoManagement, UserManagement, WebsiteManagement, ProjectManagement, and BaseDatabaseManagement classes
    • Added 5 test methods for LogIt, PyBasher, NcbiFTPClient, and Multiprocess classes
    • Total of ~705 lines of new test code across three test files
  • Docstrings added to Orthologs module

Fixed

  • Fixed typo in FullUtilities.__init__(): Ortho0logUtils → OrthologUtils (resolves AttributeError)
  • Fixed missing docstrings across codebase
  • Fixed various test issues and code coverage gaps

Changed

  • Updated Python version requirements and examples
  • Refactored code structure (#177)
  • Moved templates to .github directory
  • Updated Python tasks configuration

[1.0.0b1] - Development

Added

  • Test infrastructure improvements and codecov integration
  • GitHub Actions CI/CD pipeline replacing Travis CI
  • pytest configuration and test suite expansion
  • Test GPCR dataset for testing
  • PyBasher commands for bash operations
  • Tarfile member sanitization for security (#173)

Changed

  • Removed Travis CI in favor of GitHub Actions
  • Updated Python version support (3.9, 3.10, 3.11)
  • Upgraded Biopython version
  • Bumped dependencies: tqdm (4.25.0 → 4.66.3), jinja2, werkzeug, sqlalchemy

Fixed

  • Fixed tarfile member sanitization in extractall() (#173)
  • Fixed various test failures and code coverage issues
  • Fixed requirements.txt security vulnerabilities (#179, #175, #176, #170, #169, #168)
  • Fixed Cookies tests and Oven/CookBook text issues
  • Fixed log level color formatting
  • Fixed Flask version requirements and psutil requirement

[0.9.0a2] - Previous Release

Added

  • Initial test suite
  • Basic CI/CD setup

Changed

  • Package structure and organization

Version History Notes

  • 1.0.0b2: Latest release (2025-12-02) - Test coverage improvements and bug fixes
  • 1.0.0b1: Previous beta release - Test infrastructure and CI/CD improvements
  • 0.9.0a2: Previous tagged release (alpha)